Plastic microfluidics enabling two-dimensional protein separations in proteome analysis

ABSTRACT

The invention provides a microfluidic apparatus for performing  2 -D biomolecular separations. The microfluidic  2 -D device may include first and second planar substrates which include at least a first dimension microchannel extending in a first direction and an array of second dimension microchannels extending in a second direction, preferably, orthogonal to the first dimension. The ends of at least some of the microchannels are in fluid communication with a plurality of reservoirs. The substrates may further include a number of microchannels and reservoirs. The reservoirs are in electrical communication with a plurality of electrodes and voltage power sources. The device enables two dimensional separations of proteins and other biomolecules. According to another aspect of the invention, an isoelectric point based separation is enabled in a first dimension, and a size based separation in a second dimension.

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority from U.S. provisional patent application serial No. 60/287,754 filed on May 1, 2001, which is incorporated by reference in its entirety.

FIELD OF THE INVENTION

[0002] The invention relates to a microfluidic apparatus and methods for using the apparatus to perform two-dimensional (2-D) protein separations.

BACKGROUND OF THE INVENTION

[0003] Existing protein analysis technology is largely based upon two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), which has undeniably assumed a major role and is central to much of what is now described as “proteomics.” Typically, proteins are separated by charge in a first dimension, based on isoelectric focusing in a pH gradient medium, and by size in a second dimension, based on molecular weight in a polyacrylamide gel containing sodium dodecyl sulfate (SDS). When proteins are radiolabeled, or stained, their positions in the gel are detected by autoradiography, or densitometry, respectively.

[0004] Despite the selectivity of 2-D PAGE, existing techniques are a collection of manually intensive procedures and time-consuming tasks prone to irreproducibility and poor quantitative accuracy. Thus, automated, high resolution, rapid, reproducible, and ultrasensitive 2-D separation techniques would be advantageous for large-scale analysis of proteins.

[0005] Microfluidic platforms offer fast, accurate, and low cost electrokinetic systems for high-throughput 2-D PAGE. One drawback of existing systems is a lack of methodology to detect protein separations in microchannels. Performance of the isoelectric focusing and the size based separation can be monitored by detecting the proteins in microchannels. A robust detection system of proteins in microchannels, is not only important for identification of proteins, but also important for quantification of proteins, with accuracy and resolution.

[0006] Another drawback of the application of existing microfluidic techniques to 2-D PAGE devices is a lack of methods to introduce different separation media into different dimensions in the same unit. Performing both charge and size based separations in one miniaturized 2-D PAGE device is desirable for high-throughput purpose.

[0007] Another drawback of the application of existing microfluidic techniques to 2-D PAGE devices is a lack of methods to transfer proteins simultaneously from first to second dimensions without significant loss in resolution. In existing methods, protein analytes are continuously sampled in the first dimension and transferred to the second dimension. To date, sufficient resolution has not been achieved using existing methods.

[0008] These and other drawbacks exist.

SUMMARY OF THE INVENTION

[0009] One advantage of the invention is that it overcomes these and other drawbacks in existing systems by providing a microfluidic apparatus for performing 2-D biomolecular separations. The microfluidic 2-D device may comprise first and second planar substrates which include at least a first dimension microchannel extending in a first direction and an array of second dimension microchannels extending in a second direction, preferably, orthogonal to the first dimension. The ends of at least some of the microchannels are in fluid communication with a plurality of reservoirs. The substrates may further comprise a number of microchannels and reservoirs. The reservoirs are in electrical communication with a plurality of electrodes and voltage power sources. The device enables two dimensional separations of proteins and other biomolecules. According to another aspect of the invention, an isoelectric point based separation is enabled in a first dimension, and a size based separation in a second dimension.

[0010] Another advantage of the invention is that it enables introduction of two different media in different microchannels of the same 2-D microfluidic device (e.g., a media for isoelectric point based separation, and a media for size based separation). In one embodiment, a pressure filling technique may be used to introduce the two different media. Electroosmotic or other electrokinetic pumping may also be used to introduce the two different media. In some embodiments, a polymeric membrane sandwiched between the upper and the lower microchannels may serve as a hydrodynamic barrier, enabling the introduction of two different separation media in the upper and the lower microchannels. Other filling approaches may be used.

[0011] Another advantage of the invention is that it enables simultaneous transfer of proteins from first dimension microchannels to second dimension microchannels (e.g., by changing the electric potentials at the reservoirs connected to the microchannels). Any separation accomplished in the first dimension may be completely retained upon transfer to the second dimension. In some embodiments, the transfer of material (e.g. proteins) from the first to the second dimension may be achieved by hydrodynamic pressure at the reservoirs connecting first dimension microchannels. In other embodiments, isoelectric focused proteins in the first dimension may be electrokinetically injected into the second dimension, by altering the electric potentials at the reservoirs connecting microchannels. This simultaneous transfer approach also significantly simplifies the procedures compared to those involved in continuous sampling and separation of the eluants from the first dimension.

[0012] Another advantage of the invention is that it enables high resolution detection of proteins in microchannels. In one embodiment, proteins may be covalently labeled with a florescent dye. During first and second dimension separations, the labeled proteins may be monitored using a florescent detector attached to the microfluidic system. In some embodiments, microchannels fabricated by polydimethylsiloxane (PDMS) substrates may be used which provide low florescence background during detection and enable better signal to background resolution. According to another embodiment of the invention, laser induced florescent detection (LIFD) may be employed for the detection of SDS-25 protein complexes using non-covalent, environment-sensitive, fluorescent probes.

[0013] Another advantage of the invention is that it enables integration of 2-D microfluidic networks formed in plastic substrates (e.g., using template imprinting, injection molding, laser machining, or a combination of these technologies) with LIFD and mass spectrometry detection for automation, high throughput, reproducibility, robustness, and ultrahigh resolution. These capabilities are advantageous for large-scale proteome analysis and for “differential display” of protein expressions under various physiological conditions.

[0014] The microfluidic 2-D PAGE of the present invention may be advantageous for the study of organisms having fully sequenced genomes, and may identify proteins (and their modifications in many cases) as well as provide quantitative measurements of expression levels. Other uses will be apparent.

[0015] These and other features and advantages of the invention will be more fully appreciated from the detailed description of the preferred embodiments and the drawings attached hereto. It is also to be understood that both the foregoing general description and the following detailed description are exemplary and not restrictive of the scope of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

[0016]FIG. 1 is a schematic of microfluidic 2-D PAGE device with inlet and outlet reservoirs according to one embodiment of the invention.

[0017]FIG. 2 is a schematic of microfluidic 2-D PAGE device lacking second dimensional inlet reservoir according to one embodiment of the invention.

[0018]FIG. 3 is a schematic of microfluidic 2-D PAGE with tertiary channels for electrokinetic transfer according to one embodiment of the invention.

[0019]FIG. 4 is a schematic of a microfluidic apparatus with voltage control microchannels according to one embodiment of the invention.

[0020]FIG. 5 is a schematic of a microfluidic apparatus comprising voltage control microchannel combined with second-dimension outlet reservoir according to one embodiment of the invention.

[0021]FIG. 6 is a schematic of a microfluidic apparatus with voltage control microchannels intersecting tertiary or second-dimension microchannels according to one embodiment of the invention.

[0022]FIG. 7 is a schematic of a microfluidic apparatus with groups of tertiary or second-dimension microchannels according to one embodiment of the invention.

[0023]FIG. 8 is a schematic of a microfluidic apparatus with groups of tertiary or second-dimension microchannels merging into single common microchannels according to one embodiment of the invention.

[0024]FIG. 9 is a schematic of a microfluidic apparatus with electrically resistive elements intersecting tertiary or second-dimension microchannels according to one embodiment of the invention.

[0025]FIG. 10 is a schematic microfluidic 2-D PAGE with a polymeric membrane strip for introduction of two different media according to one embodiment of the invention.

[0026]FIG. 11 is a schematic of laser-induced fluorescence detection setup for line-based fluorescence detection in second dimension of a microchannel array according to one embodiment of the invention.

DETAILED DESCRIPTION

[0027] According to one embodiment of the invention as illustrated in FIG. 1, for example, a microfluidic 2-D gel electrophoresis apparatus is provided. Microfluidic 2-D gel electrophoresis apparatus may comprise a first planar substrate 1 containing one or more first-dimension microchannels 3 for first dimension separation, as well as a second planar substrate 2 (bonded to first planar substrate 1) to provide enclosure for one or more second-dimension microchannels 4 for second dimension separation.

[0028] According to one embodiment, the first-dimension microchannel 3 may extend in a first direction, while an array of one or more second-dimension microchannels 4 may extend from, or intersect with, the first-dimension microchannel 3 in a second direction. Preferably the second direction is orthogonal to the first direction. The first-dimension microchannel 3 may have a first end 3 a and a second end 3 b. Similarly, an array of one or more second-dimension microchannels 4 may each have a first end 4 a and a second end 4 b.

[0029] According to one embodiment the first end 4 a of the one or more second-dimension microchannels 4 may intersect the first-dimension microchannel 3 at various locations along the length of the first dimension microchannel.

[0030] According to one embodiment, as illustrated in FIG. 1, the apparatus may further comprise one or more reservoirs (5, 6, 7, 8) and voltage sources (V13, V14, V15, V16) associated with each of the reservoirs, respectively. For example, a first reservoir 5 may be in fluid communication with a first end 3 a of the first microchannel 3, and a second reservoir 6 may be in fluid communication with a second end 3 b of the first microchannel 3. Additionally, a third reservoir 7 may be in fluid communication with a first end 4 a of each of the second dimension microchannels 4, and a fourth reservoir 8 may be in fluid communication with a second end 4 b of the second dimension microchannels 4. In other embodiments, some of which are described herein, different configurations of microchannels and reservoirs may be used. Not all embodiments may use 4 reservoirs. More or less may be used.

[0031] According to one embodiment of the invention, the one or more reservoirs (5-8) may be formed in the first 1 or second 2 substrate, and a plurality of separation electrodes (9, 10, 11, 12) may be provided. A first end (indicated schematically) of the separation electrodes (9-12) may be located in electrical communication with the reservoirs 5-8, respectively. A second end (indicated schematically) of the separation electrodes 9-12 may be attached to one or more high voltage power supplies (V13, V14, V15, V16). One or more of electrodes 9-12 may also be connected to ground potential (e.g., ˜0 Volts) (not shown in the figure).

[0032] As illustrated in FIG. 1, the device has one or more inlet 5 and outlet 6 reservoirs at the ends of the first microchannel 3, and one or more inlet 7 and outlet reservoirs 8 at the ends of the second dimension microchannels 4. Other configurations may be used. For example, in one embodiment (as illustrated in FIG. 2), the first ends 4 a of the one or more second dimension microchannels 4 may terminate at one or more points between the first and second ends (3 a, 3 b) of the first dimension microchannel 3. In this embodiment, no second dimension inlet reservoir is used.

[0033] In another embodiment, as illustrated in FIG. 3, one or more second-dimension separation outlet reservoirs 8 may intersect the first end 4 a of the one or more second-dimension microchannels 4, and one or more tertiary inlet reservoirs 10 may intersect the first end 11 a of the one or more tertiary microchannels 11. The second end 11 b of the one or more tertiary microchannels 11 may terminate at one or more points between the first and second ends (3 a, 3 b) of the first dimension microchannel 3, and the first ends 4 a of the one or more second dimension microchannels 4 may terminate at one or more points between the first and second ends (3 a, 3 b) of the first dimension microchannel 3. In this embodiment, the one or more points at which the second ends (4 b) of the tertiary microchannels 11 and second dimension microchannels 4 terminate at the first dimension microchannel 3 may be staggered. Preferably, the number of tertiary microchannels 11 is equal to one more than the number of secondary microchannels 4, and the one or more points at which the first ends 4 a of the second dimension microchannels 4 terminate at the first dimension microchannel 3 are staggered from the one or more points at which the second ends 11 b of the tertiary microchannels 11 terminate at the first dimension microchannel 3 by half the distance between adjacent tertiary microchannels 11. In this embodiment, the one or more second dimension separation inlet reservoirs 7 may be omitted.

[0034] In some embodiments, microchannels (e.g., 3, 4) may have depth to width ratio of approximately 1:3. Other ratios and dimensions may be used. For example, microchannels with an average depth of 10 μm may have an average width of 30 μm. However, both depth and width preferably range from 5 to 200 μm. For illustrative purpose, the width mentioned herein is from trapezoidal shaped microchannel cross-sections. Other shapes for microchannel cross-sections may be used, for example rectangular, circular, or semi-circular cross-sections. The microchannels (e.g. 3, 4) can be any suitable length. A preferred length ranges from about 1 to about 10 cm. Other lengths may be used. Some embodiments may have other microchannel dimensions for various applications.

[0035] In some embodiments, a plastic substrate such as poly(methylmethacrylate) (PMMA) or polycarbonate may be used for fabrication of the microfluidic 2-D apparatus.

[0036] In one embodiment, a polydimethylsiloxane (PDMS) layer combined with a rigid substrate is used for fabrication of the 2-D microfluidic apparatus. Non-plastic materials such as glass or silica may also be used to fabricate the 2-D microfluidic apparatus of the present invention.

[0037] Spacing between the intersections determines the size of the sample plug being introduced into the second dimension microchannel array 4. The extent of resolution loss during the transfer step is mainly dependent upon the spacing and focused protein bandwidth achieved from isoelectric focusing in the first dimension microchannel 3.

[0038] According to one embodiment, microchannels (e.g., 3, 4) may be filled with any suitable carrier ampholyte solution for first dimension separation and any gel solution preferably with SDS for second dimension separation of proteins. A preferred voltage for separation of proteins range from 100 V/cm to 1000 V/cm. A high voltage power supply may be attached to a second end of a selected number of the one or more separation electrodes (e.g., electrodes 9-12). Due to the extremely large surface area to volume ratio of microchannels (e.g., 3, 4) for efficient heat dissipation, the application of high electric voltage enables rapid and excellent separation of proteins in the microfluidic network. In some embodiments, microfluidic device of the present invention is used for separating DNA, peptides, and other biological or chemical composites.

[0039] According to one aspect of the invention, the 2-D plastic microfluidic device separates protein analytes with ultrahigh resolution based on their differences in isoelectric point and size. As illustrated in FIG. 1, one or more microchannels 3 extending from left to right in the figure and connecting one or more reservoirs 5 and 6 may be employed for performing a non-native isoelectric focusing separation in a first dimension. Once the first dimension separation is complete, the material (e.g. proteins) may be transferred into a microchannel array connecting one or more reservoirs 8 for performing a parallel and high throughput size-dependent separation. The transfer to the second dimension may occur virtually simultaneously in each microchannel of the second dimension array of microchannels 4. In some embodiments, one or more reservoirs 10 (as illustrated in FIG. 3) at the end of one or more tertiary microchannels 11 may be used for introducing the electrophoresis buffer containing SDS and SYPRO fluorescent dyes during electrokinetic transfer of proteins from first dimension to second dimension.

[0040] To monitor the performance of isoelectric focusing in first dimension microchannels 3, proteins may be covalently labeled with a suitable florescent dye and detected by a suitable florescence detector. An example of a fluorescent dye is 5-carboxy fluorescein succinimidyl ester which may be used to label the proteins. Other dyes or labeling techniques may be used. An example of a detector is a Zeiss fluorescence microscope. Other detectors and detection techniques may be used. Because of the large number of amino groups on protein molecules, very small amounts of fluorescein dye is needed. These labeled proteins may be denatured and reduced at approximate concentration of 1 mg/ml for each protein. The proteins may be prepared in a suitable solution (e.g., a solution including urea, dithiothreitol, and Tris-HCl with approximate concentrations of 8M, 100 mM and 0.1 M respectively) with a pH preferably ranging from 4 to 10. The protein solution may be kept under a nitrogen atmosphere for about four hours in room temperature. The denatured and reduced proteins may be desalted using a column preferably by PD-10 column. Eluted proteins may be dried preferably by vacuum and stored at a preferred temperature of about −20° C. These proteins may be reconstituted in the solution containing carrier ampholytes (approximately 2% pharmalyte 3-10) and urea (between 1 and 3 M) for performing non-native isoelectric focusing. Plastic microchannels made out of PDMS substrate are advantageous for isoelectric focusing because they are optically transparent at the wavelengths required for the fluorescence detection of proteins and they provide low fluorescence background. Other materials may be used.

[0041] According to one aspect of the invention, two different media are introduced in a 2-D microfluidic network for performing two dimensional separations of proteins. Isoelectric focusing in the first dimension involves the use of carrier ampholytes for the creation of pH gradient in the microchannel. However, size-dependent separation of SDS-protein complexes in the second dimension is based on their differences in electrophoretic mobility inside a polymer sieving matrix.

[0042] In one embodiment, a pressure filling approach may be used for introducing two different media into the at least one first dimension microchannel and array of second dimension microchannels respectively. Gel solutions may be introduced into microchannel arrays (e.g., 3, 4) by applying pressure in reservoirs. As illustrated in FIG. 2, reservoir 8 and the connecting microchannel array 4 may be filled with a polymer gel solution. Various polymers, including polyacrylamide, polyethylene oxide, and branched dextran, can be employed for preparing the gel solution. The gel solution may be introduced into the array by applying pressure at reservoir 8. The flow velocity may be controlled by the pressure gradient, the viscosity of the solution, and the channel dimensions. The filling process may be monitored by adding a preferred fluorescent dye, ethidium bromide (excitation: 514 nm; emission: 604 nm), into the gel solution and using a preferred fluorescent detector, Zeiss fluorescence microscope, equipped with a computer controlled moving stage. The filling may be stopped as soon as the gel solution reaches the intersections of the microchannel array and the channel connecting reservoirs 5 and 6. The solution containing carrier ampholytes for isoelectric focusing separation may then be introduced via pressure from reservoir 5 for filling the channel connecting reservoirs 5 and 6. Because of the low viscosity in the ampholyte solution, the pressure needed for introducing the ampholyte solution is much lower than that required for pushing a polymer gel solution. Thus, a 2-D plastic microfluidic network may be filled with two different separation media using this two-step pressure filling approach. It should be noted that any suitable fluorescent dye may be added to gel and any suitable detector may be used to monitor the filling process.

[0043] In another embodiment, the entire plastic microfluidic network may initially be filled with a polymer gel solution by pressure. The pressure level required for filling the microfluidic network depends upon the cross-sectional dimensions and lengths of the microchannels, in addition to the viscosity of the gel solution. In the case of embodiments where the bonding strength between the top and bottom layers of the device is not sufficient to hold the device together during high-pressure filling, an external force may be applied to hold the layers together during the filling process. The filling of the microfluidic network is followed by removal of the polymer gel in the microchannels connecting reservoirs 5 and 6 as illustrated in FIG. 2. Removal of gel in the first-dimension microchannel may be achieved by applying a pressure to reservoir 5 while leaving reservoir 6 open, and closing all other reservoirs in the device to prevent loss of gel from the second-dimension microchannels. In another embodiment, removal of the gel is achieved using an electroosmotic process. The electroosmotic removal process may be induced by applying a positive electric voltage ranging from 1 to 10 kV at reservoirs 5 containing a preferred salt, NaOH, solution. The speed and completeness of electroosmotic removal approach may be monitored by adding preferred dye ethidium bromide into the gel solution and using a preferred fluorescence detector Zeiss fluorescence microscope equipped with a computer controlled moving stage. The removal speed is expected to increase as the section of microchannel containing NaOH instead of polymer gel solution increases. As soon as the removal process is complete, the solution containing any carrier ampholytes for the isoelectric focusing may then be introduced via pressure from reservoir 5 for filling the first dimension channel connecting reservoirs 5 and 6.

[0044] In yet another embodiment, a preferred polymeric membrane, polyvinylidene fluoride (PVDF), sandwiched between the upper and lower microchannels may serve as a hydrodynamic barrier, providing the initial filling of two different separation media in the upper and lower microchannels. As illustrated in FIG. 10, 2-D protein separation platform may comprise the upper substrate (A) containing two or more reservoirs (5 and 6) for isoelectric focusing in the upper channel 3 and two or more reservoirs (7 and 8) for size based separation in the lower channel array 4, one or more microchannels 3 for performing isoelectric focusing separation, a polymeric membrane strip (B), and the lower substrate containing a microchannel array 4 for performing size-based separation (C). In FIG. 10, D illustrates the assembly of 2-D protein separation platform. According to one aspect of the present invention, the pressure needed for pushing a solution through the membrane with a pore diameter of approximately 0.1 μm may be at least 50 times higher than that required for introducing an aqueous solution into the microchannels. Furthermore, the solutions may take a lower flow-resistance path. Thus, two different electrophoresis media may be separately filled in the upper and lower microchannels. According to another aspect of the present invention, the membrane (B) at the intersections between the upper and the lower microchannels may also serve as injection ports when pressure applied at both ends of the upper microchannel for transferring proteins from the first to the second dimension. In analogy to a dead-end microfiltration process, the focused protein zones in the upper channel may simultaneously permeate through the exposed membrane areas at the nearby intersections.

[0045] The methods of the present invention for introducing two different media in the same microfluidic device may also be used for other media in two dimensions for separating DNA, peptides, and other chemical and biological composites.

[0046] According one aspect of the present invention, focused proteins in the first dimension are simultaneously transferred to the second dimension by hydrodynamic pressure. To fulfill the requirements of a comprehensive 2-D separation system, the two dimensions should be orthogonal, and any separation accomplished by the first dimension should ideally be retained upon transfer to the second dimension. First dimensional microchannels 3 connecting reservoirs 5 and 6 (as illustrated in FIG. 2) may be disconnected from the high voltage power supply as soon as the focusing is complete in the first dimension. Equal pressure may then be applied at reservoirs 5 and 6 to drive the solution containing focused protein analytes into the parallel microchannel array. Since the flow resistance in the gel filled microchannel array is extremely high, a constant hydrostatic pressure may be therefore in place across the entire isoelectric focusing channel during this step. Thus, the transfer process may be similar to dead-end membrane filtration. In some embodiments, a highly viscous polymer gel solution at the intersections between the first and second separation dimensions may serve as the individual injection ports for quantitative transfer of focused protein bands. In other embodiments, a polymeric membrane serves as the injection ports for transfer of proteins.

[0047] In another aspect of the present invention, focused proteins in the first dimension (e.g., 3) may be electrokinetically transferred to the second dimension (e.g. 4) using end reservoirs (e.g., 5, 6). As soon as the focusing is complete in the first separation dimension, the voltage may be turned off and the solution containing catholyte in reservoir 6 (as illustrated FIG. 2) may be replaced with a Tris buffer containing SDS and a florescent dye, preferably, SYPRO orange. A positive electric potential may then be reapplied briefly at reservoir 5 for rapid electrokinetic injection and filling of SDS and dye within the first separation dimension (e.g., 3), followed by the incubation of focused proteins with SDS and dye for approximately 5-10 minutes. Since the focused proteins from the first separation dimension (e.g., 3) (non-native isoelectric focusing) may be already denatured and reduced, the rapid formation of SDS-protein complexes may not only prepare protein analytes for size based separation in the second dimension (e.g., 4), but may also establish the foundation for performing electrokinetic protein transfer. The SDS-protein complexes may be electrokinetically injected by grounding reservoir 5 while applying two separate positive potentials at reservoir 6 and 8 using two high voltage power supplies (V14, V16). The smaller positive potential at reservoir 6 may be employed to continuously drive the proteins in the first dimension toward the channel junctions. As soon as the proteins reach the channel junctions, the larger positive potential at reservoir 8 may commence the electrokinetic injection of focused proteins into the second separation dimension.

[0048] In yet another aspect of the present invention, focused proteins in the first dimension may be electrokinetically transferred to the second dimension using tertiary reservoirs 10 as illustrated in FIG. 3. This method may involve the use of a set of tertiary microchannels 11 to introduce SDS and a florescent dye, preferably, SYPRO orange. In this method, as soon as the focusing is complete in the first separation dimension (e.g., 3), the voltage may be turned off and the solution in the one or more reservoirs labeled 10 (as illustrated in FIG. 3) may be replaced with a Tris buffer containing SDS and dye. With the potentials at reservoirs 5 and 6 floating, a positive electric potential may then be applied briefly at reservoir 8 for rapid electrokinetic injection and filling of SDS and dye from the tertiary microchannels 11 leading from reservoir 10, through the portion of the first-dimension separation channels 3 between the tertiary microchannels 11, and partially into the second dimension separation channels 4. Once this portion of the microchannel network may be filled, the proteins focused in the first dimension may be incubated with newly introduced SDS and dye for approximately 5-10 minutes. Since the focused proteins from the first separation dimension (non-native isoelectric focusing) may be already denatured and reduced, the rapid formation of SDS-protein complexes may not only prepare protein analytes for the size-based separation in second dimension, but may also establish the foundation for performing electrokinetic protein transfer. After incubation, the SDS-protein complexes may be electrokinetically injected by grounding reservoir 10 while applying a positive potential at reservoir 8 and letting reservoirs 5 and 6 float. Because each tertiary microchannel 11 may intersect the first-dimension microchannel in between two adjacent second-dimension microchannels 4, the applied field may force the majority of SDS-protein complexes that lie within the first dimension microchannel 3 between the extent of the second-dimension microchannels 4 to be transferred into the second dimension (e.g., 4) electrokinetically.

[0049] In some embodiments, electrokinetic transfer method may be performed to transfer DNA, peptides, and other chemical or biological composites from one dimension to another dimension of the gel electrophoresis system. As used herein, “electrokinetic transfer method” includes a method or a system which transfer materials from a channel and/or chamber containing structure in one dimension to similar structures in other dimensions, through the application of electric fields to the materials, thereby causing the transfer of the materials.

[0050] According to one embodiment of the invention, as illustrated in FIG. 3, a grounding voltage may be applied to the one or more tertiary reservoirs 10, while a high voltage may be applied to the one or more second-dimension outlet reservoirs 8. All other reservoirs may be disconnected from any voltage source. Pursuant to this arrangement, a high electric field is applied along the length of the one or more second-dimension separation microchannels 4, with said electric field passing from the one or more tertiary microchannels 11 through the one or more regions of the first-dimension microchannel 3 between adjacent tertiary 11 and second-dimension microchannels 4, and into the one or more second-dimension microchannels 4, thereby causing biomolecules within the first-dimension microchannel 3 to be drawn into the one or more second-dimension microchannels 4 to ensure efficient transfer of the biomolecules from the first-dimension microchannel 3 into the one or more second dimension microchannels 4.

[0051] According to another aspect of the invention, one or more intersection control voltages may be applied to the one or more second-dimension separation outlet reservoirs 8 (as illustrated in FIG. 3) or tertiary inlet reservoirs 10 (as illustrated in FIG. 3), and the one or more second-dimension separation inlet reservoirs 7 (as illustrated in FIG. 1). This may control the electric field lines at the intersection of the one or more first-dimension separation microchannels 3 and the one or more second-dimension separation microchannels 4 in such a manner that the distribution of biomolecules undergoing separation during the first-dimension separation step are not substantially affected by the intersections.

[0052] According to an embodiment, as depicted in FIG. 4, the one or more intersection control voltages may be applied using a plurality of voltage sources, wherein one voltage source (not shown in the figure) may be applied to the one or more inlet reservoirs 35 of the one or more voltage control microchannels 36, and a second voltage source may be connected to the one or more outlet reservoirs 37 of the one or more voltage control microchannels 36 to generate a potential gradient along fluid within the one or more voltage control microchannels 36. The geometry of the one or more voltage control microchannels 36 may be selected such that the intersection control voltage at the one or more intersections of the voltage control microchannels 36 and the second-dimension microchannels 4 and/or tertiary microchannels 11 is set by the voltages applied at the voltage control reservoirs (35, 37). Further, the one or more intersection control voltages may be chosen such that the voltage within the one or more second-dimension microchannels 4 and/or tertiary microchannels 11 near the intersection of the one or more first-dimension separation microchannels 3 and the one or more second-dimension separation microchannels 4 (connected to the reservoir at which the intersection control voltage is applied) is slightly different than the voltage within the intersection itself. In this embodiment, the one or more tertiary inlet reservoirs 10 are omitted.

[0053] According to another aspect of the invention, depicted in FIG. 5, a single voltage control microchannel 36 may be combined with a second-dimension outlet reservoir 8.

[0054] According to another aspect of the invention, depicted in FIG. 6, one or more voltage control microchannels 36 may intersect the one or more tertiary microchannels 11, and one or more voltage control microchannels 36 may intersect the one or more second-dimension microchannels 4.

[0055] According to another aspect of the invention, depicted in FIG. 7, groups of one or more tertiary microchannels 11 may intersect one or more tertiary inlet reservoirs 10. Similarly, groups of one or more second-dimension microchannels 4 may intersect one or more second-dimension outlet reservoirs 8.

[0056] According to another aspect of the invention, depicted in FIG. 8, groups of one or more tertiary microchannels 11 may merge into a single common tertiary microchannel 52, which intersects the one or more tertiary inlet reservoirs 10. Similarly, groups of one or more second-dimension microchannels 4 may merge into a single common second-dimension microchannel 51, which intersects the one or more second-dimension outlet reservoirs 8.

[0057] According to one embodiment, the one or more intersection control voltages may be applied using a plurality of voltage sources, wherein one voltage source may be connected to the first end of a first resistive element, and a second voltage source may be connected to the second end of the first resistive element to generate a potential gradient along the first resistive element. The resistive element may placed in electrical contact with the one or more second-dimension separation inlet reservoirs such that the intersection control voltage in each reservoir is set by the voltage of the first resistive element at the point of electrical contact. Further, the one or more intersection control voltages may be chosen such that the voltage near the intersection of the one or more first-dimension separation microchannels 3 and the one or more second-dimension separation microchannels 4 (connected to the reservoir at which the intersection control voltage is applied) is slightly different than the voltage within the intersection itself.

[0058] A third voltage source may be connected to the first end of a second resistive element, and a fourth voltage source may be connected to the second end of the second resistive element to generate a potential gradient along the second resistive element. The second resistive element may then be placed in electrical contact with the one or more second-dimension separation inlet reservoirs, such that the intersection control voltage in each reservoir is set by the voltage of the second resistive element at the point of electrical contact. The one or more intersection control voltages may be chosen such that the voltage near the intersection of the one or more first-dimension separation microchannels 3 and the one or more second-dimension separation microchannels 4 (connected to the reservoir at which the intersection control voltage is applied) is slightly lower than the voltage within the intersection itself.

[0059] According to another aspect of the invention, depicted in FIG. 9, one or more electrically-resistive elements (42, 43) such as a thin-film metal, wire, conductive polymer, or similar material may intersect the one or more tertiary microchannels 11 and the one or more second-dimension microchannels 4, with the one or more resistive elements (42, 43) in electrical contact with the fluid within the microchannels. One or more voltage sources (V44, V45, V46, V47) are applied at each end of the one or more resistive elements (42, 43), thereby creating a voltage drop along the length of the resistive elements (42, 43). Since the one or more resistive elements (42, 43) are in electrical contact with the fluid at the points of intersection with the microchannels, the local voltage at each point in the microchannel may be controlled in this manner, with the voltages defined by the one or more voltage sources (V44, V45, V46, V47) and the resistance of the one or more resistive elements (42, 43).

[0060] One of the advantages of the present invention is integration of a optical source device and an image capturing device for monitoring the detection of SDS-protein complexes near the end of second dimension microchannel array using non-covalent, environment-sensitive, fluorescent probes.

[0061] For example, florescent probes such as SYPRO orange (excitation: 470 nm, emission: 570 nm) or SYPRO red (excitation: 550 nm, emission: 630 nm) may be employed for pre-electrophoretic staining of proteins. As shown in FIG. 11, an argon ion laser 21 may be used for excitation. The output beam from the laser is diverged, collimated to span the entire second dimension microchannel array, and focused vertically in a narrow line across the array. This is achieved using a (diverging) 2.5 cm focal length plano-concave cylindrical lens 23 in series with a (collimating) 10 cm focal length plano-convex cylindrical lens 24 and a (focusing) 5.0 cm focal length plano convex cylindrical lens 25, respectively. The fluorescence in each channel of the array is independently monitored using a charged-coupled device (CCD) camera 27 with a 50 mm macro Nikon camera lens. The CCD sensor is comprised of 26 μm pixels positioned in a 1024×128 array. The system is arranged so that a single column of pixels on the sensor is designated to measure the fluorescence intensity emitted from each individual channel over time. A holographic notch filter may be located in front of the image capturing device to filter out any laser scattering. It should be noted that any suitable detecting devices and image capturing devices known to one skilled in the art can be used with microfluidic 2-D PAGE system for monitoring the protein separations in the microchannel array.

[0062] According one aspect of the present invention, microfluidic 2-D PAGE may be integrated with mass spectrometry employing matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) for integrating protein separation, quantification, identification, and sequencing processes. Electrospray ionization may be integrated into the microfluidic network by extending the second-dimension microchannels to the outer edge of the device to form electrospray tips, or by combining traditional silica capillary electrospray tips into the microfluidic system. The integrated system offers large-scale analysis of proteins and “differential display” proteomics for comparisons of protein expression under various environmental and physiological conditions.

[0063] Other embodiments, uses and advantages of the invention will be apparent to those skilled in the art from consideration of the specification and practice of the invention disclosed herein. The specification should be considered exemplary only, and the scope of the invention is accordingly intended to be limited only by the following claims. 

We claim:
 1. A microfluidic apparatus for performing two-dimensional biomolecular separations, the apparatus comprising: at least one first dimension microchannel; an array of second dimension microchannels; means for performing a first separation in the first dimension microchannel to produce a separated sample; means for transferring the separated sample to the second dimension microchannels; and means for introducing a first media in the first dimension microchannel and a second media into the array of second dimension microchannels.
 2. The apparatus of claim 1 wherein the first media is a media for enabling separation based on isoelectric focusing.
 3. The apparatus of claim 1 wherein the second media is a media for enabling size-based separation.
 4. The apparatus of claim 1 wherein the means for introducing comprises pressure filling means.
 5. The apparatus of claim 1 wherein the means for introducing comprises means for filling each of the first dimension microchannel and second dimension microchannels with a second media, electroosmotically removing the second media from one of the first dimension microchannel or the second dimension microchannels and introducing a first media therein.
 6. The apparatus of claim 1 further comprising a hydrodynamic barrier between the first dimension microchannel and second dimension microchannels to enable each to be filled with a different media.
 7. The apparatus of claim 1, wherein the biomolecular separation is to be performed on a biomolecular material and the biomolecular material comprises protein, the first dimension separation is a isoelectric point-based separation and the second dimension separation is a size-based separation.
 8. The apparatus of claim 1 wherein the first dimension separation is substantially retained upon transfer to the second dimension.
 9. The apparatus of claim 1, wherein the first media comprises a media for isoelectric point based separation.
 10. The apparatus of claim 1, wherein the second media comprises a media for size based separation.
 11. The apparatus of claim 1, wherein the first media comprises a media for isoelectric focusing in the first dimension, comprising carrier ampholytes for the creation of pH gradient in the first microchannel.
 12. The apparatus of claim 1, wherein the second media comprises a media for size based separation of SDS-protein complexes in the second dimension based on their differences in electrophoretic mobility inside a polymer sieving matrix.
 13. The apparatus of claim 1, wherein the second media is a sieving matrix selected from the group consisting of: cross-linked polyacrylamide, linear polyacrylamide, polydimethylamide, N-acrylamoniethoxyethanol, hydroxyethylcellulose [HEC], poly(ethylene glycol), poly(ethylene oxide) [PEO], poly(vinylpyrrolidone) [PVP], or nonionic polymeric surfactants (n-alkyl polyoxyethylene ethers).
 14. The apparatus of claim 1, further comprising a detector placed near a second end of the array of second-dimension separation microchannels for differential display of protein expressions.
 15. The apparatus of claim 1, further comprising a detector capable of monitoring substantially all of the full length and breadth of the array of second-dimension separation microchannels for differential display of protein expressions.
 16. The apparatus of claim 1, further comprising a detector to monitor the performance of isoelectric focusing in the at least one first dimension microchannel, wherein proteins may be covalently labeled with a suitable florescent dye and detected by a suitable florescence detector.
 17. The apparatus of claim 1, further comprising a detector to monitor the performance of isoelectric focusing in first dimension microchannels, wherein proteins in a biomolecular sample may be covalently labeled with a suitable florescent dye and detected by a suitable florescence detector and the microchannels are formed from a substrate optically transparent at the wavelengths used for the fluorescence detection.
 18. The apparatus of claim 1 further comprising an integrated optical detection system.
 19. The apparatus of claim 1 further comprising an integrated laser-induced fluorescence detection system.
 20. The apparatus of claim 1, wherein first ends of the second dimension microchannels in the array of second-dimension microchannels terminate at the at least one first-dimension microchannel at one or more points between first and second ends of the at least one first-dimension microchannel, and wherein at least one outlet reservoir is in fluid communication with second ends of the second-dimension microchannels.
 21. The apparatus of claim 1 wherein the second-dimension microchannels have first and second ends and the at least one first dimension microchannel intersects the second dimension microchannels at a position somewhere between the first and second ends of the second-dimension microchannels.
 22. The apparatus of claim 1 wherein an inlet reservoir is in fluid communication with the first end of the second dimension microchannels and an outlet reservoir is in fluid communication with the second end of the second dimension microchannels.
 23. The apparatus of claim 1, wherein the first ends of the second-dimension microchannels terminate at the at least one first-dimension microchannel and further comprising an array of tertiary microchannels, wherein a second end of the tertiary microchannels terminate at the at least one first-dimension microchannel.
 24. The apparatus of claim 23 wherein points at which the second-dimension microchannels intersect with the at least one first-dimension microchannel are staggered with respect to points at which the tertiary microchannels intersect with the at least one first-dimension microchannel.
 25. The apparatus of claim 23 wherein one or more outlet reservoirs are in fluid communication with second ends of the second dimension microchannels and one or more inlet reservoirs are in fluid communication with first ends of the tertiary microchannels.
 26. The apparatus of claim 23 wherein groups of the array of tertiary microchannels merge into a first end of a smaller number of one or more merged tertiary microchannels, and wherein one or more outlet reservoirs are in fluid communication with the second end of the second-dimension microchannels and one or more inlet reservoirs are in fluid communication with a second end of the merged tertiary microchannels.
 27. The apparatus of claim 26 wherein a length of the merged tertiary microchannels is significantly larger than a length of a voltage-control microchannel, thereby increasing an electrical resistivity of the merged tertiary microchannels compared with an electrical resistivity of the voltage-control microchannels when filled with a similar conductive solution.
 28. The apparatus of claim 23 wherein groups of the array of second-dimension microchannels merge into a first end of a smaller number of one or more second-dimension microchannels, and wherein one or more outlet reservoirs are in fluid communication with a second end of the merged second-dimension microchannels and one or more inlet reservoirs are in fluid communication with the second end of the tertiary microchannels.
 29. The apparatus of claim 28 wherein a length of the merged second-dimension microchannels is substantially larger than a length of a voltage-control microchannel, thereby increasing an electrical resistivity of the merged second-dimension microchannels compared with an electrical resistivity of the voltage-control microchannels when filled with a similar conductive solution.
 30. The apparatus of claim 1 further comprising a voltage control microchannel, wherein a cross-sectional area of the voltage control microchannels is similar to a cross-sectional area of the at least one first-dimension microchannel, thereby creating a similar electrical resistivity in each channel when filled with a similar conductive solution.
 31. The apparatus of claim 23 further comprising a voltage control microchannel, wherein a cross-sectional area of the voltage control microchannel is substantially smaller than a cross-sectional area of the second-dimension microchannels and tertiary microchannels, thereby increasing an electrical resistivity of the second-dimension and tertiary microchannels compared with an electrical resistivity of the voltage-control microchannel when filled with a similar conductive solution.
 32. The apparatus of claim 1 further comprising first and second planar substrates wherein the first and second planar substrates comprise glass.
 33. The apparatus of claim 1 further comprising first and second planar substrates wherein the first and second planar substrates comprise plastic.
 34. The apparatus of claim 1 further comprising first and second planar substrates wherein the first and second planar substrates comprise polycarbonate plastic.
 35. The apparatus of claim 1 further comprising first and second planar substrates wherein the first and second planar substrates comprise a combination of dissimilar materials including glass, polydimethylsiloxane (PDMS), plastic, or silicon.
 36. The apparatus of claim 1 wherein the at least one first dimension microchannel and the second dimension microchannels have an inner width of between about 5 μm and about 200 μm.
 37. The apparatus of claim 1, wherein at least one first dimension microchannel and the second dimension microchannels have an average inner width of between about 5 μm and about 80 μm.
 38. The apparatus of claim 1 wherein the at least one first dimension microchannel and the second dimension microchannels have an average inner width of between about 5 μm and about 20 μm.
 39. The apparatus of claim 1 wherein the at least one first dimension microchannel and the second dimension microchannels possess different average widths.
 40. The apparatus of claim 1 wherein the at least one first-dimension microchannel has an average width substantially smaller than the second-dimension microchannels.
 41. The apparatus of claim 1 wherein the second-dimension microchannels have an average width substantially smaller than the at least one first-dimension microchannel.
 42. The apparatus of claim 1 wherein the at least one first dimension microchannel and the second dimension microchannels have an inner depth of between about 5 μm and about 200 μm.
 43. The apparatus of claim 1 wherein the at least one first dimension microchannel and the second dimension microchannels have an average inner depth of between about 5 μm and about 80 μm.
 44. The apparatus of claim 1 wherein the at least one first dimension microchannel and the second dimension microchannels have an average inner depth of between about 5 μm and about 20 μm.
 45. The apparatus of claim 1 wherein the at least one first dimension microchannel and the second dimension microchannels possess different average inner depths.
 46. The apparatus of claim 1 wherein the at least one first-dimension microchannel has an average inner depth substantially smaller than the average inner depths of the second-dimension microchannels.
 47. The apparatus of claim 1 wherein the second-dimension microchannels have average inner depths substantially smaller than the average inner depth of the at least one first-dimension microchannel.
 48. The apparatus of claim 1, wherein the at least one first-dimension microchannel is between about 1 cm and about 50 cm long.
 49. The apparatus of claim 1 wherein the at least one first-dimension microchannel is between about 1 cm and about 4 cm long.
 50. The apparatus of claim 1 wherein the second-dimension microchannels are between about 1 cm and about 50 cm long.
 51. The apparatus of claim 1 wherein the second-dimension microchannels are between about 1 cm and about 4 cm long.
 52. A microfluidic apparatus for performing two-dimensional protein separations, the apparatus comprising: at least one first dimension microchannel; an array of second dimension microchannels; means for performing a first biomolecular separation in the first dimension microchannel to produce a separated sample; and means for simultaneously transferring the separated sample to the second dimension microchannels.
 53. A microfluidic apparatus for performing two-dimensional protein separations, the apparatus comprising: at least one first dimension microchannel; an array of second dimension microchannels; means for performing a first biomolecular separation in the first dimension microchannel to produce a separated sample; and means for electrokinetically transferring the separated sample simultaneously to the second dimension microchannels.
 54. A microfluidic apparatus for performing two-dimensional biomolecular separations, the apparatus comprising: at least one first dimension microchannel; an array of second dimension microchannels; means for performing a first biomolecular separation in the first dimension microchannel to produce a separated sample; means for transferring the separated sample simultaneously to the second dimension microchannels; and means for performing a second separation in the second dimension microchannels; and means for introducing a first media in the first dimension microchannel and a second media into the array of second dimension microchannels.
 55. A microfluidic apparatus for performing two-dimensional protein separations, the apparatus comprising: at least one first dimension microchannel for performing a first protein separation; an array of one or more second dimension microchannels for performing a second separation; an array of one or more tertiary microchannels; one or more electrodes that intersect the one or more second dimension microchannels and the one or more tertiary microchannels; one or more voltage sources operatively connected to the one or more electrodes to control the voltage at the points of intersection with the microchannels.
 56. A microfluidic apparatus for performing two-dimensional protein separations, the apparatus comprising: at least one first dimension microchannel for performing a first protein separation; an array of one or more second dimension microchannels for performing a second separation; an array of one or more tertiary microchannels; one or more voltage-control microchannels that intersect the one or more second dimension microchannels and the one or more tertiary microchannels; one or more voltage sources operatively connected to the one or more voltage-control microchannels to control the voltage at the points of intersection with the second-dimension and tertiary microchannels.
 57. A method for performing two-dimensional biomolecular separations with a microfluidic apparatus, the method comprising the steps of: providing at least one first dimension microchannel; providing an array of second dimension microchannels; performing a first separation in the first dimension microchannel to produce a separated sample; transferring the separated sample to the second dimension microchannels; and introducing a first media in the first dimension microchannel and a second media into the array of second dimension microchannels.
 58. The method of claim 57 wherein the first media is a media for enabling separation based on isoelectric focusing.
 59. The method of claim 57 wherein the second media is a media for enabling size-based separation.
 60. The method of claim 57 wherein the step of introducing comprises pressure filling the second-dimension microchannels with a second media without filling the first-dimension microchannel, followed by pressure filling the first-dimension microchannel with a first media.
 61. The method of claim 57 wherein the step of introducing comprises filling each of the first dimension microchannel and second dimension microchannels with a second media, electroosmotically removing the second media from one of the first dimension microchannel or the second dimension microchannels and introducing a first media therein.
 62. The method of claim 57 further comprising the step of providing a hydrodynamic barrier between the first dimension microchannel and second dimension microchannels to enable each to be filled with a different media.
 63. A method for performing two-dimensional protein separation with a microfluidic apparatus, the method comprising the steps of: providing at least one first dimension microchannel; providing an array of second dimension microchannels; performing a first protein separation in the first dimension microchannel to produce a separated sample; and simultaneously transferring the separated sample to the second dimension microchannels.
 64. A method for performing two-dimensional protein separation with a microfluidic apparatus, the method comprising the steps of: providing at least one first dimension microchannel; providing an array of second dimension microchannels; performing a first protein separation in the first dimension microchannel to produce a separated sample; and electrokinetically transferring the separated sample simultaneously to the second dimension microchannels.
 65. A method for performing two-dimensional biomolecular separations with a microfluidic apparatus, the method comprising the steps of: providing at least one first dimension microchannel; providing an array of second dimension microchannels; means for performing a first biomolecular separation in the first dimension microchannel to produce a separated sample; means for transferring the separated sample simultaneously to the second dimension microchannels; performing a second separation in the second dimension microchannels; and introducing a first media in the first dimension microchannel and a second media into the array of second dimension microchannels.
 66. A method for performing two-dimensional biomolecular separations with a microfluidic apparatus, the method comprising the steps of: providing at least one first dimension microchannel; providing an array of second dimension microchannels; providing an array of one or more tertiary microchannels; providing one or more electrodes that intersect the one or more second dimension microchannels and the one or more tertiary microchannels; operating one or more voltage sources operatively connected to the one or more electrodes to control the voltage at the points of intersection with the microchannels.
 67. A method for performing two-dimensional biomolecular separations with a microfluidic apparatus, the method comprising the steps of: providing at least one first dimension microchannel; providing an array of second dimension microchannels; providing an array of one or more tertiary microchannels; providing one or more voltage-control microchannels that intersect the one or more second dimension microchannels and the one or more tertiary microchannels; operating one or more voltage sources operatively connected to the one or more voltage-control microchannels to control the voltage at the points of intersection with the microchannels. 